Not counting the ports of older games, I'd have to say there are quite a few really good games.
Metroid Fusion and Metroid Zero Mission are two great games that have polished the controls and gameplay of the 2D Metroid to its finest.
Castlevania: Circle of the Moon did a great job at a Castleroid while still not being a SotN ripoff. It also has an appealing difficulty.
Castlevania: Aria of Sorrow adds just the right amount of collection element into the game. The soul system is wonderful, and the only problem is that the game is
far too easy, even on Hard mode.
Surprisingly, F-Zero: Maximum Velocity is actually a great game, with extreme difficulty, but the learning curve isn't too absurd.
A somewhat overlooked platformer that is great fun and also has an interesting fighting engine is Dragonball: Advanced Adventure. Nice!
Wario Ware Inc. is just pure genius.
One of the greatest puzzle games of all time gets some recognition on GBA, Pokémon Puzzle League is a Tetris Attack kind of game with lots of gameplay in it.
Now, if you're counting ports as well, we have SMB3 (the greatest game of all time), well all of the SMA titles are actually solid, as well as FF V and VI, and Zelda, to name a few. On top of those, we have loads of Famicom Mini titles, which add even more to the already huge pool of great games